Table 1.

Summary of the stage‐specific transcriptomes (A–D) of the three Zymoseptoria tritici isolates

Isolate	Infection stage	Sample	Time point (dpi)	No. of filtered reads	No. of reads mapped to genome	% reads mapped to genome	No. of genes RPKM ≥2a	No. of genes RPKM ≥10a
Zt05b	A	Zt05_Ta_A_01	3	107,507,137	15,213,307	14.15	9,302	7,455
		Zt05_Ta_A_02		81,479,903	10,509,515	12.90
	B	Zt05_Ta_B_01	8	113,732,295	15,057,425	13.24	9,404	7,623
		Zt05_Ta_B_02		128,271,704	14,856,314	11.58
	C	Zt05_Ta_C_01	13	91,298,814	26,756,807	29.31	9,538	7,982
		Zt05_Ta_C_02		135,198,719	34,329,884	25.39
	D	Zt05_Ta_D_01	20	86,100,462	41,871,582	48.63	9,585	7,914
		Zt05_Ta_D_02		119,101,106	76,123,086	63.91
Zt09c	A	Zt09_Ta_A_01	4	129,342,007	5,868,572	4.54	9,435	7,482
		Zt09_Ta_A_02		92,711,865	5,582,561	6.02
	B	Zt09_Ta_B_01	11	96,767,482	5,034,677	5.20	9,718	7,910
		Zt09_Ta_B_02		103,428,015	5,964,566	5.77
	C	Zt09_Ta_C_01	13	121,529,652	31,264,373	25.73	9,892	8,220
		Zt09_Ta_C_02		93,253,633	27,790,773	29.80
	D	Zt09_Ta_D_01	20	110,296,264	84,263,562	76.40	9,867	7,949
		Zt09_Ta_D_02		101,757,635	75,044,880	73.75
Zt10d	A	Zt10_Ta_A_01	6	93,557,587	4,895,650	5.23	8,814	7,219
		Zt10_Ta_A_02		91,111,840	4,836,535	5.31
	B	Zt10_Ta_B_01	11	94,828,793	5,951,869	6.28	9,068	7,407
		Zt10_Ta_B_02		110,255,245	7,896,227	7.16
	C	Zt10_Ta_C_01	13	86,652,710	20,804,110	24.01	9,241	7,742
		Zt10_Ta_C_02		91,070,127	8,620,099	9.47
	D	Zt10_Ta_D_01	24	98,493,807	29,939,216	30.40	9,062	7,308
		Zt10_Ta_D_02		93,690,628	34,607,371	36.94

Overview of RNA‐seq datasets including time point of sampling, number of sequenced reads post filtering, number of mapped reads, percentage of mapped reads, and numbers of transcribed genes.

^aRPKM values were calculated using Cuffdiff2 and are normalized over all infection stages within the respective isolate (normalization method: geometric, dispersion method: per‐condition).

^b11,138 genes of IPO323 (94.08%) found by nucleotide blast for Zt05.

^c11,754 of the 11,839 genes predicted and annotated for IPO323 (Grandaubert et al., 2015); 85 genes located on chromosome 18 were not considered.

^d10,745 genes of IPO323 (90.76%) found by nucleotide blast for Zt10.